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Meehan GR, Herder V, Allan J, Huang X, Kerr K, Mendonca DC, Ilia G, Wright DW, Nomikou K, Gu Q, Molina Arias S, Hansmann F, Hardas A, Attipa C, De Lorenzo G, Cowton V, Upfold N, Palmalux N, Brown JC, Barclay WS, Filipe ADS, Furnon W, Patel AH, Palmarini M. Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathog 2023; 19:e1011589. [PMID: 37934791 PMCID: PMC10656012 DOI: 10.1371/journal.ppat.1011589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/17/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve throughout the coronavirus disease-19 (COVID-19) pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2, BA.2.75 and EG.5.1. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75 and EG.5.1) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.
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Affiliation(s)
- Gavin R. Meehan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Xinyi Huang
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Diogo Correa Mendonca
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Georgios Ilia
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Derek W. Wright
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sergi Molina Arias
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Florian Hansmann
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Germany
| | - Alexandros Hardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, North Mymms, United Kingdom
| | - Charalampos Attipa
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, United Kingdom
| | | | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Nicole Upfold
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, United Kingdom
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
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Patsikas M, Adamama-Moraitou K, Thomas A, Soultani C, Chrissogonidis I, Fotiadou A, Trikoupi G, Papadopoulou P, Ilia G, Kosmas P, Farmakis P. Pre- and post-treatment computed tomographic findings of a primary intranasal transmissible venereal tumor in a canine patient. J BIOL REG HOMEOS AG 2018; 32:571-576. [PMID: 29921382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A two-year-old, female intact, cross-breed dog presented with a two-month history of nasal discharge. Computed tomography (CT) demonstrated obliteration of both nasal cavities by soft tissue density, destruction of the nasal and ethmoidal turbinates, and lysis of the frontal and palatine bones and maxilla. Frontal sinuses and maxillary recesses were obscured by soft tissue/fluid density. Histopathological examination of the mass was diagnostic of transmissible venereal tumor. The dog was clinically normal 3 months after treatment initiation with vincristine sulphate and amoxicillin/clavulanate. Six months after the completion of treatment no mass-like lesion was demonstrated in CT sections. Nasal cavities, maxillary recesses and frontal sinuses were filled with air. The reticular turbinate nasal plexus appeared atrophic with focal loss of the nasal turbinates on both sides. The ethmoidal turbinates were well-defined; however, focal loss of turbinates was also seen. Lysis of the frontal and palatine bones were still evident.
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Affiliation(s)
- M Patsikas
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - K Adamama-Moraitou
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - A Thomas
- Private Practice, Thessaloniki, Greece
| | | | - I Chrissogonidis
- School of Medicine, Aristotle University of Thessaloniki, Greece
| | - A Fotiadou
- Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, Middlesex, UK
| | - G Trikoupi
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - P Papadopoulou
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - G Ilia
- School of Medicine, Aristotle University of Thessaloniki, Greece
| | - P Kosmas
- Private Practice, Thessaloniki, Greece
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Affiliation(s)
- B. Maranescu
- Institute of Chemistry Timisoara of the Romanian Academy, 24 Mihai Viteazu Bvd., 300223, -Timisoara, Romania
| | - A. Visa
- Institute of Chemistry Timisoara of the Romanian Academy, 24 Mihai Viteazu Bvd., 300223, -Timisoara, Romania
| | - G. Ilia
- Institute of Chemistry Timisoara of the Romanian Academy, 24 Mihai Viteazu Bvd., 300223, -Timisoara, Romania
- West University of Timisoara, 16 Pestalozzi Street, 300115 Timisoara, Romania
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